MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : 12dgr140_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM4108 STM2285 STM3526 STM0322 STM4567 STM4326 STM1511 STM3529 STM1620 STM3542 STM4485 STM1448 STM0772 STM4585 STM3704 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM0977   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.255979 (mmol/gDw/h)
  Minimum Production Rate : 0.031380 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.820928
  EX_pi_e : 0.227009
  EX_k_e : 0.045462
  EX_so4_e : 0.031225
  EX_mg2_e : 0.002021
  EX_fe2_e : 0.001876
  EX_ca2_e : 0.001213
  EX_cl_e : 0.001213
  EX_cobalt2_e : 0.000808
  EX_cu2_e : 0.000808
  EX_mn2_e : 0.000808
  EX_mobd_e : 0.000808
  EX_zn2_e : 0.000808

Product: (mmol/gDw/h)
  EX_h2o_e : 25.903977
  EX_co2_e : 18.815679
  EX_h_e : 2.324614
  EX_ac_e : 0.141718
  Auxiliary production reaction : 0.031380
  EX_glyclt_e : 0.012799
  EX_glyald_e : 0.000177
  DM_hmfurn_c : 0.000114

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 27-Sep-2023
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